Difference between revisions of "Team:Evry Paris-Saclay/Parts"
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<p>During this project, our team designed the following basic parts:</p> | <p>During this project, our team designed the following basic parts:</p> | ||
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| − | <h2 class="anchor" style="font-weight:800;" id='composite_parts'>COMPOSITE PARTS</h2> | + | <h2 class="anchor" style="font-weight:800; text-align:center;" id='composite_parts'>COMPOSITE PARTS</h2> |
<p>During this project, our team designed the following composite parts:</p> | <p>During this project, our team designed the following composite parts:</p> | ||
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| − | <h2 class="anchor" style="font-weight:800;" id='part_collection'>PART COLLECTION</h2> | + | <h2 class="anchor" style="font-weight:800; text-align:center;" id='part_collection'>PART COLLECTION</h2> |
<p style="font-size:15px;">In our project we tried to repurpose a peptide communication machinery from a phage of the Gram-positive <em>Bacillus subtilis</em> to the cells of Gram-negative <em>Escherichia coli</em>, and quickly discovered that crossing the inter-species barrier in bioengineering is a challenging task. This Part Collection consists of a series of promoter variants designed to debug the mechanism of transcriptional regulation in the pAimX promoter that is key to the signalling system. The Collection helped us successfully identify an internal terminator, investigate a potential anti-termination mechanism, and build a hybrid promoter that converts the native transcriptional activator (AimR) into a transcriptional repressor.</p> | <p style="font-size:15px;">In our project we tried to repurpose a peptide communication machinery from a phage of the Gram-positive <em>Bacillus subtilis</em> to the cells of Gram-negative <em>Escherichia coli</em>, and quickly discovered that crossing the inter-species barrier in bioengineering is a challenging task. This Part Collection consists of a series of promoter variants designed to debug the mechanism of transcriptional regulation in the pAimX promoter that is key to the signalling system. The Collection helped us successfully identify an internal terminator, investigate a potential anti-termination mechanism, and build a hybrid promoter that converts the native transcriptional activator (AimR) into a transcriptional repressor.</p> | ||
Revision as of 21:07, 15 October 2018
BASIC PARTS
During this project, our team designed the following basic parts:
Coding sequences
| Part Number | Part Name |
|---|---|
| BBa_K2675000 | AimR-Phi3T |
| BBa_K2675001 | AimP-Phi3T |
| BBa_K2675002 | OmpA-SAIRGA |
| BBa_K2675003 | PelB-SAIRGA |
| BBa_K2675004 | TAT-SAIRGA |
| BBa_K2675005 | sfGFP |
| BBa_K2675006 | sfGFP-LVAtag |
Ribosomal binding sites (RBS)
| Part Number | Part Name |
|---|---|
| BBa_K2675010 | Synthetic RBS designed for AimR of Phi3T |
| BBa_K2675011 | Synthetic RBS designed for AimP of Phi3T |
| BBa_K2675012 | Synthetic RBS designed for OmpA-SAIRGA |
| BBa_K2675013 | Synthetic RBS designed for PelB-SAIRGA |
| BBa_K2675014 | Synthetic RBS designed for TAT-SAIRGA |
| BBa_K2675015 | Synthetic RBS designed for sfGFP |
| BBa_K2675016 | Synthetic RBS designed for sfGFP |
| BBa_K2675017 | Synthetic RBS designed for sfGFP |
Promoters
| Part Number | Part Name |
|---|---|
| BBa_K2675020 | pAimX(full) promoter of phage phi3T |
| BBa_K2675021 | pAimX(short) promoter of phage phi3T |
| BBa_K2675022 | pAimX(short)-J23110 hybrid promoter |
| BBa_K2675023 | pAimX(full-1)-J23110 hybrid promoter |
| BBa_K2675024 | pAimX(full-2)-J23110 hybrid promoter |
| BBa_K2675025 | pAimX(full-3)-J23110 hybrid promoter |
| BBa_K2675026 | J23110 truncated promoter (-10 only) + cloning Scar |
| BBa_K2675090 | pAimX(full-noTerminator-v1) promoter of phage phi3T |
| BBa_K2675091 | pAimX(full-noTerminator-v2) promoter of phage phi3T |
| BBa_K2675092 | pAimX(full-noTerminator-v3) promoter of phage phi3T |
| BBa_K2675093 | pAimX(full-noTerminator-v4) promoter of phage phi3T |
| BBa_K2675094 | pAimX(full-noTerminator-v5) promoter of phage phi3T |
| BBa_K2675095 | pAimX(full-noTerminator-v6) promoter of phage phi3T |
| BBa_K2675096 | pAimX(full-noTerminator-v7) promoter of phage phi3T |
| BBa_K2675097 | pAimX(full-noTerminator-v8) promoter of phage phi3T |
Terminators
| Part Number | Part Name |
|---|---|
| BBa_K2675030 | L3S2P56 Terminator |
| BBa_K2675031 | L3S2P21 Terminator |
and a Golden Gate adapter
| Part Number | Part Name |
|---|---|
| BBa_K2675070 | Golden Gate adapter |
COMPOSITE PARTS
During this project, our team designed the following composite parts:
| Part Number | Part Name |
|---|---|
| BBa_K2675040 | AimR-Phi3T expression cassette |
| BBa_K2675041 | AimP-Phi3T expression cassette |
| BBa_K2675042 | OmpA-SAIRGA expression cassette |
| BBa_K2675043 | PelB-SAIRGA expression cassette |
| BBa_K2675044 | TAT-SAIRGA expression cassette |
| BBa_K2675080 | Golden Gate adapter + sfGFP |
| BBa_K2675081 | Golden Gate adapter + sfGFP-LVAtag |
| BBa_K2675050 | sfGFP-LVAtag expression cassette under the contol of pAimX(full) promoter of phage phi3T |
| BBa_K2675051 | sfGFP-LVAtag expression cassette under the contol of pAimX(short) promoter of phage phi3T |
| BBa_K2675052 | sfGFP-LVAtag expression cassette under the contol of pAimX(short)-J23110 hybrid promoter |
| BBa_K2675053 | sfGFP-LVAtag expression cassette under the contol of pAimX(full-1)-J23110 hybrid promoter |
| BBa_K2675054 | sfGFP-LVAtag expression cassette under the contol of pAimX(full-2)-J23110 hybrid promoter |
| BBa_K2675055 | sfGFP-LVAtag expression cassette under the contol of pAimX(full-3)-J23110 hybrid promoter |
| BBa_K2675056 | sfGFP-LVAtag expression cassette under the contol of J23110 promoter |
| BBa_K2675057 | sfGFP-LVAtag expression cassette under the contol of J23110 and pAimX(full) promoter of phage phi3T |
| BBa_K2675058 | sfGFP-LVAtag expression cassette under the contol of J23110 and pAimX(short) promoter of phage phi3T |
| BBa_K2675059 | sfGFP-LVAtag expression cassette under the contol of J23110 and pAimX(short) promoter of phage phi3T |
| BBa_K2675101 | sfGFP-LVAtag expression cassette under the contol of J23110 and pAimX(full-noTerminator-v1) promoter of phage phi3T |
| BBa_K2675102 | sfGFP-LVAtag expression cassette under the contol of J23110 and pAimX(full-noTerminator-v2) promoter of phage phi3T |
| BBa_K2675103 | sfGFP-LVAtag expression cassette under the contol of J23110 and pAimX(full-noTerminator-v3) promoter of phage phi3T |
| BBa_K2675104 | sfGFP-LVAtag expression cassette under the contol of J23110 and pAimX(full-noTerminator-v4) promoter of phage phi3T |
| BBa_K2675105 | sfGFP-LVAtag expression cassette under the contol of J23110 and pAimX(full-noTerminator-v5) promoter of phage phi3T |
| BBa_K2675106 | sfGFP-LVAtag expression cassette under the contol of J23110 and pAimX(full-noTerminator-v6) promoter of phage phi3T |
| BBa_K2675107 | sfGFP-LVAtag expression cassette under the contol of J23110 and pAimX(full-noTerminator-v7) promoter of phage phi3T |
| BBa_K2675108 | sfGFP-LVAtag expression cassette under the contol of J23110 and pAimX(full-noTerminator-v8) promoter of phage phi3T |
| BBa_K2675060 | sfGFP expression cassette under the contol of pAimX(full) promoter of phage phi3T |
| BBa_K2675061 | sfGFP expression cassette under the contol of pAimX(short) promoter of phage phi3T |
| BBa_K2675062 | sfGFP expression cassette under the contol of pAimX(short)-J23110 hybrid promoter |
| BBa_K2675063 | sfGFP expression cassette under the contol of pAimX(full-1)-J23110 hybrid promoter |
| BBa_K2675064 | sfGFP expression cassette under the contol of pAimX(full-2)-J23110 hybrid promoter |
| BBa_K2675065 | sfGFP expression cassette under the contol of pAimX(full-3)-J23110 hybrid promoter |
| BBa_K2675066 | sfGFP expression cassette under the contol of J23110 promoter |
PART COLLECTION
In our project we tried to repurpose a peptide communication machinery from a phage of the Gram-positive Bacillus subtilis to the cells of Gram-negative Escherichia coli, and quickly discovered that crossing the inter-species barrier in bioengineering is a challenging task. This Part Collection consists of a series of promoter variants designed to debug the mechanism of transcriptional regulation in the pAimX promoter that is key to the signalling system. The Collection helped us successfully identify an internal terminator, investigate a potential anti-termination mechanism, and build a hybrid promoter that converts the native transcriptional activator (AimR) into a transcriptional repressor.
| Part Number | Part Name |
|---|---|
| BBa_K2675020 | pAimX(full) promoter of phage phi3T |
| BBa_K2675021 | pAimX(short) promoter of phage phi3T |
| BBa_K2675022 | pAimX(short)-J23110 hybrid promoter |
| BBa_K2675023 | pAimX(full-1)-J23110 hybrid promoter |
| BBa_K2675024 | pAimX(full-2)-J23110 hybrid promoter |
| BBa_K2675025 | pAimX(full-3)-J23110 hybrid promoter |
| BBa_K2675090 | pAimX(full-noTerminator-v1) promoter of phage phi3T |
| BBa_K2675091 | pAimX(full-noTerminator-v2) promoter of phage phi3T |
| BBa_K2675092 | pAimX(full-noTerminator-v3) promoter of phage phi3T |
| BBa_K2675093 | pAimX(full-noTerminator-v4) promoter of phage phi3T |
| BBa_K2675094 | pAimX(full-noTerminator-v5) promoter of phage phi3T |
| BBa_K2675095 | pAimX(full-noTerminator-v6) promoter of phage phi3T |
| BBa_K2675096 | pAimX(full-noTerminator-v7) promoter of phage phi3T |
| BBa_K2675097 | pAimX(full-noTerminator-v8) promoter of phage phi3T |
When placed upstream of a reporter gene, promoters from this Part Collection showed variable transcription strengths and degrees of regulation that provided valuable insights for our project and facilitated the porting of the peptide communication machinery from B. subtilis to E. coli.
To build this Part Collection the BBa_K2675080 and BBa_K2675081 were a key tool.
| Part Number | Part Name |
|---|---|
| BBa_K2675050 | sfGFP-LVAtag expression cassette under the contol of pAimX(full) promoter of phage phi3T |
| BBa_K2675051 | sfGFP-LVAtag expression cassette under the contol of pAimX(short) promoter of phage phi3T |
| BBa_K2675052 | sfGFP-LVAtag expression cassette under the contol of pAimX(short)-J23110 hybrid promoter |
| BBa_K2675053 | sfGFP-LVAtag expression cassette under the contol of pAimX(full-1)-J23110 hybrid promoter |
| BBa_K2675054 | sfGFP-LVAtag expression cassette under the contol of pAimX(full-2)-J23110 hybrid promoter |
| BBa_K2675055 | sfGFP-LVAtag expression cassette under the contol of pAimX(full-3)-J23110 hybrid promoter |
| BBa_K2675057 | sfGFP-LVAtag expression cassette under the contol of J23110 and pAimX(full) promoter of phage phi3T |
| BBa_K2675058 | sfGFP-LVAtag expression cassette under the contol of J23110 and pAimX(short) promoter of phage phi3T |
| BBa_K2675059 | sfGFP-LVAtag expression cassette under the contol of J23110 and pAimX(short) promoter of phage phi3T |
| BBa_K2675101 | sfGFP-LVAtag expression cassette under the contol of J23110 and pAimX(full-noTerminator-v1) promoter of phage phi3T |
| BBa_K2675102 | sfGFP-LVAtag expression cassette under the contol of J23110 and pAimX(full-noTerminator-v2) promoter of phage phi3T |
| BBa_K2675103 | sfGFP-LVAtag expression cassette under the contol of J23110 and pAimX(full-noTerminator-v3) promoter of phage phi3T |
| BBa_K2675104 | sfGFP-LVAtag expression cassette under the contol of J23110 and pAimX(full-noTerminator-v4) promoter of phage phi3T |
| BBa_K2675105 | sfGFP-LVAtag expression cassette under the contol of J23110 and pAimX(full-noTerminator-v5) promoter of phage phi3T |
| BBa_K2675106 | sfGFP-LVAtag expression cassette under the contol of J23110 and pAimX(full-noTerminator-v6) promoter of phage phi3T |
| BBa_K2675107 | sfGFP-LVAtag expression cassette under the contol of J23110 and pAimX(full-noTerminator-v7) promoter of phage phi3T |
| BBa_K2675108 | sfGFP-LVAtag expression cassette under the contol of J23110 and pAimX(full-noTerminator-v8) promoter of phage phi3T |
| BBa_K2675060 | sfGFP expression cassette under the contol of pAimX(full) promoter of phage phi3T |
| BBa_K2675061 | sfGFP expression cassette under the contol of pAimX(short) promoter of phage phi3T |
| BBa_K2675062 | sfGFP expression cassette under the contol of pAimX(short)-J23110 hybrid promoter |
| BBa_K2675063 | sfGFP expression cassette under the contol of pAimX(full-1)-J23110 hybrid promoter |
| BBa_K2675064 | sfGFP expression cassette under the contol of pAimX(full-2)-J23110 hybrid promoter |
| BBa_K2675065 | sfGFP expression cassette under the contol of pAimX(full-3)-J23110 hybrid promoter |